LAMMPS (7 Aug 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style fourier
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
  5 = max # of 1-2 neighbors
  10 = max # of 1-3 neighbors
  16 = max # of 1-4 neighbors
  20 = max # of special neighbors
  special bonds CPU = 0.000747919 secs
  read_data CPU = 0.0168228 secs

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
  1250 = # of size 2 clusters
  0 = # of size 3 clusters
  250 = # of size 4 clusters
  0 = # of frozen angles
  find clusters CPU = 0.000355244 secs

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
  G vector (1/distance) = 0.382011
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0325934
  estimated relative force accuracy = 9.8154e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 34263 16000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
      50    4712.9507    4669.1606    324.15119    43.790082     1798.561    670.61319    690.16967   -3276.9493      811.643    1305983.2   -1306633.5    17164.771    48631.318    442.24313    116.13094 
     100    2865.9139    3726.4166    258.70226   -860.50272    968.87546    749.70761    860.70151   -3270.7784    427.14745    1306104.7   -1306700.9    15017.273    48631.318    385.10628    35.845353 
     150    1982.6673     3535.974      245.481   -1553.3068    764.86116    768.15837    658.70182   -3278.7906    108.49859    1306136.5   -1306711.2    16495.352    48631.318    378.64023    10.723986 
     200    1440.0277    3240.5932    224.97452   -1800.5656    687.71813    791.29356    643.82915   -3276.9293   -99.549986    1306172.9   -1306719.8    13234.476    48631.318    350.46321    3.7468464 
     250    1103.2915     3018.496    209.55567   -1915.2045    677.97905    825.32748    642.78891   -3278.0801    -226.1853    1306168.5   -1306725.5    8774.9103    48631.318    327.36313    1.8722119 
     300    789.07159    2827.1716    196.27319      -2038.1    735.96101    852.72545    589.14167   -3280.0357   -374.66018      1306169   -1306730.2    2259.1028    48631.318    306.85585    1.3262598 
     350    599.10023    2732.3739    189.69197   -2133.2737    677.67006    863.22888    565.41674   -3280.5231   -403.28794    1306177.4   -1306733.2     7989.222    48631.318    296.64126    1.1534418 
     400    428.26436    2591.2884    179.89727   -2163.0241    676.18745    849.24505    612.34065   -3277.4703   -457.85799    1306173.6   -1306739.1    7282.1438    48631.318    281.34719    1.0502762 
     450    307.26859    2534.2468    175.93722   -2226.9782    712.17636    853.98862    578.01327   -3279.7731   -533.87422    1306179.7   -1306737.2    1897.9643    48631.318    275.11317    1.0980929 
     500    234.60959    2495.1082    173.22007   -2260.4987    707.43541    878.25753    547.08402   -3281.2756   -549.04991    1306176.5   -1306739.5    2683.0639    48631.318    270.85452    1.0984718 
     550    203.34751    2445.6535    169.78673    -2242.306    669.03724    892.85034    599.20664   -3279.0757   -559.81157    1306175.9   -1306740.4    4512.9992    48631.318    265.49465    1.0628812 
     600    205.63573    2526.5892     175.4056   -2320.9535    685.64073    887.97693    557.42296   -3280.0332   -597.34755    1306167.8   -1306742.5    2999.5823    48631.318    274.29935     1.064682 
     650    176.23031    2526.3124    175.38638   -2350.0821    714.15285    895.42115    540.39191   -3280.8567   -636.27783    1306165.7   -1306748.6    871.68316    48631.318     274.2807    1.0442089 
     700    106.97524    2441.1059    169.47101   -2334.1306    697.16018    905.51407    564.71847   -3279.6208   -631.62324    1306159.4   -1306749.6    1953.8241    48631.318    264.98935    1.0771037 
     750    76.695104    2435.6635    169.09318   -2358.9684    672.01039    934.63351    545.64024   -3281.1075   -629.89722    1306152.4   -1306752.6    3044.0155    48631.318    264.39002    1.0932471 
     800    57.614075     2456.928    170.56945   -2399.3139    720.76364    898.68013    534.10051   -3281.5897   -659.64354    1306145.5   -1306757.1    1691.9503    48631.318    266.72089    1.0622697 
     850   -44.931126    2390.0608    165.92727   -2434.9919    708.70192    888.26851    537.13087    -3281.355   -665.17283    1306137.8   -1306760.3    123.07165    48631.318    259.45151    1.0516426 
     900   -96.878205     2358.862    163.76133   -2455.7403    672.98976    868.41571    546.69492   -3280.6939   -636.80102    1306134.5   -1306760.9    1955.7005    48631.318    256.05598      1.05337 
     950   -80.012575    2374.4497    164.84349   -2454.4623    679.59722    880.35157    548.35372   -3280.6061   -643.44517    1306125.8   -1306764.5    1510.9809    48631.318    257.72442    1.1017392 
    1000   -21.440874    2440.6729    169.44096   -2462.1138    718.56593    868.65109    555.54643   -3279.8516   -686.71673    1306126.6     -1306765   -1148.6212    48631.318    264.92977    1.1019339 
    1050     16.46903    2382.6961    165.41598   -2366.2271    712.51245    913.35848    579.81678   -3280.0559   -657.12122    1306129.3     -1306764    1004.5778    48631.318    258.64076    1.0684155 
    1100    35.847247    2483.1985    172.39325   -2447.3513    685.05704    889.42278    553.73166   -3280.0177   -663.67201    1306134.3   -1306766.2     699.1824    48631.318    269.56773    1.0838094 
    1150   -4.9817843    2431.4725    168.80223   -2436.4543    720.51056    868.17547    569.09902   -3280.5829   -677.99865    1306133.1   -1306768.7    435.19118    48631.318    263.96966    1.0303202 
    1200   -23.907197    2443.6035    169.64441   -2467.5107    684.96437    887.58483    549.43666   -3280.3144   -679.46182    1306137.2   -1306766.9    367.11148    48631.318    265.28645    1.0344036 
    1250   -16.904671    2389.9447    165.91921   -2406.8494    722.06959    902.90076    568.35616   -3280.6829   -683.32029    1306132.9   -1306769.1    76.759445    48631.318    259.41697    1.0908431 
    1300   -1.7822102    2410.2768    167.33074   -2412.0591    706.98675    904.31941    551.23506   -3280.7552   -651.51211    1306127.3   -1306769.6    1659.1113    48631.318    261.64093    1.0701648 
    1350    -3.569473    2446.3901    169.83786   -2449.9595    686.13971    894.85839    558.36242   -3279.9941   -664.59508      1306129   -1306773.7    783.32881    48631.318     265.5696    1.0709072 
    1400   -33.385576     2400.262    166.63547   -2433.6476     709.5808    890.68408    571.13105   -3280.1428   -674.51247    1306123.4   -1306773.8   -751.38571    48631.318    260.54522     1.080234 
    1450   -11.215152    2405.5409    167.00196    -2416.756    703.72038    913.21131    552.64196   -3280.9831   -649.19774    1306120.3   -1306776.4    1817.2174    48631.318    261.14741     1.031193 
    1500   -25.974102    2435.8375    169.10527   -2461.8116    689.93174    900.70619    552.63711   -3280.1497   -671.17989      1306124   -1306777.8   -98.941796    48631.318    264.45069    1.0190784 
    1550   -76.496407    2394.8126    166.25716    -2471.309    706.96953    886.06919     549.9101   -3280.8434   -659.57745    1306105.9   -1306779.7   -7.0989994    48631.318    259.95403    1.0772144 
    1600   -79.549932    2395.1114     166.2779   -2474.6614    684.11692    888.93332    562.94522   -3280.1665   -665.21744    1306114.4   -1306779.6    320.58515    48631.318    260.00641    1.0425978 
    1650   -99.702003    2360.5652    163.87957   -2460.2672    706.21244     900.9253    540.36599   -3280.2308   -655.96077    1306109.7   -1306781.3    307.35487    48631.318    256.23383    1.0666637 
    1700   -69.422658    2372.1727    164.68541   -2441.5954    676.79347    913.90473    581.60658    -3279.997   -670.33218    1306115.7   -1306779.3   -204.22848    48631.318    257.50963    1.0434075 
    1750   -80.889897    2425.3592    168.37782   -2506.2491    672.88937    911.52373    523.74733   -3280.4796   -673.90027      1306122     -1306782    965.12568    48631.318    263.26491    1.1001595 
    1800   -82.419368     2361.798    163.96515   -2444.2173    716.51571     882.9729    577.92505   -3278.9279   -671.67438    1306111.6   -1306782.6   -44.954517    48631.318    256.36957    1.0636692 
    1850   -93.715705    2373.3359    164.76616   -2467.0516    713.02466    907.03621    563.38626   -3280.2576   -693.30963    1306104.6   -1306781.5   -979.95945    48631.318    257.62543    1.0628288 
    1900    -73.60945    2449.5873    170.05983   -2523.1967    683.65116    893.94251    539.90847   -3281.4318   -680.16358      1306108   -1306787.1    598.18213    48631.318    265.91405    1.0766352 
    1950   -66.068291    2437.3691    169.21159   -2503.4374     672.5168    877.42934    573.56499    -3279.885   -668.54185    1306109.2   -1306787.7    733.05074    48631.318    264.61409    1.0224258 
    2000   -91.043979    2374.4077    164.84057   -2465.4516    692.13299    909.46192    574.60109    -3279.837   -672.33599    1306102.4   -1306791.8   -665.61581    48631.318    257.76275    1.0263294 
Loop time of 23.7656 on 4 procs for 2000 steps with 5500 atoms

Performance: 3.636 ns/day, 6.602 hours/ns, 84.155 timesteps/s
94.3% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 11.918     | 13.096     | 14.137     |  27.0 | 55.10
Bond    | 0.74012    | 0.76511    | 0.79225    |   2.9 |  3.22
Kspace  | 6.7821     | 7.8285     | 9.0172     |  35.4 | 32.94
Neigh   | 0.37249    | 0.37262    | 0.37278    |   0.0 |  1.57
Comm    | 0.70503    | 0.7188     | 0.72807    |   1.1 |  3.02
Output  | 0.0018752  | 0.0047592  | 0.013386   |   7.2 |  0.02
Modify  | 0.91164    | 0.91644    | 0.92123    |   0.5 |  3.86
Other   |            | 0.06335    |            |       |  0.27

Nlocal:    1375 ave 1381 max 1368 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost:    7803.75 ave 7856 max 7755 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs:    334465 ave 349504 max 315867 min
Histogram: 1 0 0 1 0 0 0 0 1 1

Total # of neighbors = 1337859
Ave neighs/atom = 243.247
Ave special neighs/atom = 15.6364
Neighbor list builds = 32
Dangerous builds = 0
Total wall time: 0:00:23
